Structure of RNA and Protein Synthesis

This course covers structure of RNA and protein synthesis (Translation).

RNA is also known as Ribonucleic acid. RNA molecules are single-stranded (except in some viruses) nucleic acids composed of nucleotides as DNA. They play significant role in transcription and translation (protein synthesis). Dr. Severo Ochoa discovered RNA and was awarded the Nobel Prize for Medicine in 1959.

RNA nucleotides contain three components: nitrogenous base, five carbon sugar, and phosphate group. Adenine (A), guanine (G), cytosine (C) and uracil (U) are the five nitrogenous bases (Figure 22). Adenine and guanine are purines, whereas cytosine and uracil are pyrimidines. The five carbon (pentose) sugar in RNA is ribose. Phosphate group is attached to 3′ position of one ribose and 5′ position of another.

Types of RNA

RNAs are found in our cytoplasm and are synthesized in the nucleus. There are mainly three types of RNAs.

1. Messenger RNA (mRNA): mRNA plays a significant role in transcription, where the information of DNA is utilized to synthesize protein in a cell. They constitute 5-10% of total RNA present in the cell. They carry genetic information from DNA to the ribosome (Figure 23). Messenger RNA is first synthesized by genes as nuclear heterogeneous RNA (hnRNA), varies a lot in size and molecular weight and hence they code for variety of proteins. At the end of process of transcription, mRNA is transported to the cytoplasm to complete protein synthesis.

Prokaryotic mRNA consists of 5’cap, poly A sequence, coding and non-coding regions, initiation as well as termination codon.

2. Ribosomal RNA (rRNA): Ribosomal RNA is extremely abundant and makes up to 80% of RNA found in cytoplasm. In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein. They are composed of two subunits: a large subunit and a small subunit.

Ribosomes contain a binding site for mRNA and two binding sites for tRNA on their large ribosomal subunit. During translation, small ribosomal subunit attaches to mRNA molecule. At the same time, an initiator tRNA molecule recognizes and binds to a specific codon sequence on the same mRNA molecule. A large ribosomal subunit then joins the newly formed complex. Both ribosomal subunits travel along the mRNA molecule translating the codons on mRNA into a polypeptide chain as they go

3. Transfer RNA (tRNA): These are the smallest of the three types of RNA 60-95 nucleotides long, molecular weight 18-20kD, and the secondary structure resembling a clover leaf (Figure 24). Clover leaf structure is stabilized by strong hydrogen bonds between the nucleotides. tRNA molecules are key to the translation process of mRNA sequence into amino acid sequence.

Translation

Transcription is a process of formation of ribonucleic acid (RNA) from deoxyribonucleic acid (DNA). These transcribed RNAs later get translated into proteins.

The main components of the protein synthesis are:

1. DNA
2. Three types of RNA (mRNA, rRNA, and tRNA)
3. Amino acids
4. Ribosomes
5. Enzymes

DNA contains the genetic information about the sequence of amino acids in a polypeptide chain. Structure and properties of DNA regulate and control the synthesis of proteins. messenger RNA carries the information in the form of a genetic code about the sequence of amino acids of a polypeptide chain to be synthesized. This genetic code specifies assembly of the amino acids in a polypeptide chain.

In prokaryotes, the RNA synthesis (transcription) and protein synthesis (translation) take place in the cytoplasm as they lack nucleus. However, in eukarytoes, RNA synthesis takes place in the nucleus whereas, the protein synthesis takes place in the cytoplasm. The mRNA synthesized in the nucleus is exported to cytoplasm via nucleopores.

There are three major steps involved in the process of translation (Figure 25):

1. Initiation (RNA Polymerase Binds to DNA): DNA is transcribed by an enzyme RNA polymerase or DNA dependent RNA polymerase. RNA polymerase attaches to the DNA at a specific area containing specific nucleotide sequence, called the promoter region. Hence, specific nucleotide sequences guide/regulate RNA polymerase where to begin and end the process.
2. Elongation of DNA: Specific proteins known as transcription factors unwind the DNA strand and allow RNA polymerase to transcribe only a single strand of DNA into a single stranded RNA polymer called messenger RNA (mRNA). The strand that serves as the template is called the antisense strand and the one that’s not transcribed are called sense strand. When RNA polymerase transcribes the DNA, guanine pairs with cytosine (G-C) and adenine pairs with uracil (A-U).
3. Termination: RNA polymerase moves along the DNA until it reaches a terminator sequence. RNA polymerase releases the mRNA polymer at the termination point and mRNA polymer is detach from DNA. The stop codons are UAA, UGA and UAG. There is no tRNA which can bind these codons.There are three release factors in prokaryotes, which help in chain termination. They are RF1, RF2 and RF3.

RNA Editing

RNA editing is a process of converting mRNA to RNA in the cell. RNA editing was first iden­tified in the mitochondrial gene.  This process can involve editing of either the whole gene or only a few bases. It occurs just after the process of transcription and before translation.

Several types of RNA editing are shown below:

1. Base insertion or deletion: This process involves insertion or deletion of base pairs. These alterations are mediated by specific kind of RNA called guide RNA. For example, G editing found in negative strand RNA viruses.
2. Base substitution or modification: These alterations are catalyzed by enzymes that recognize a specific target sequence of nucleotides.

For example, human APOB gene and C to U editing in plant mitochondria and chloroplasts, where de-amination of cytosine is done by enzyme cytidine deaminase.